paCalls: Methods for P/A Calls

In oligo: Preprocessing tools for oligonucleotide arrays

Description

Methods for Present/Absent Calls are meant to provide means of assessing whether or not each of the (PM) intensities are compatible with observations generated by background probes.

Usage

paCalls(object, method, ..., verbose=TRUE)
## S4 method for signature 'ExonFeatureSet'
paCalls(object, method, verbose = TRUE)
## S4 method for signature 'GeneFeatureSet'
paCalls(object, method, verbose = TRUE)
## S4 method for signature 'ExpressionFeatureSet'
paCalls(object, method, ..., verbose = TRUE)

Arguments

object	Exon/Gene/Expression-FeatureSet object.
method	String defining what method to use. See 'Details'.
...	Additional arguments passed to MAS5. See 'Details'
verbose	Logical flag for verbosity.

Details

For Whole Transcript arrays (Exon/Gene) the valid options for method are 'DABG' (p-values for each probe) and 'PSDABG' (p-values for each probeset). For Expression arrays, the only option currently available for method is 'MAS5'.

ABOUT MAS5 CALLS:

The additional arguments that can be passed to MAS5 are:

1. alpha1: a significance threshold in (0, alpha2);

2. alpha2: a significance threshold in (alpha1, 0.5);

3. tau: a small positive constant;

4. ignore.saturated: if TRUE, do the saturation correction described in the paper, with a saturation level of 46000;

This function performs the hypothesis test:

H0: median(Ri) = tau, corresponding to absence of transcript H1: median(Ri) > tau, corresponding to presence of transcript

where Ri = (PMi - MMi) / (PMi + MMi) for each i a probe-pair in the probe-set represented by data.

The p-value that is returned estimates the usual quantity:

Pr(observing a more "present looking" probe-set than data | data is absent)

So that small p-values imply presence while large ones imply absence of transcript. The detection call is computed by thresholding the p-value as in:

call "P" if p-value < alpha1 call "M" if alpha1 <= p-value < alpha2 call "A" if alpha2 <= p-value

Value

A matrix (of dimension dim(PM) if method="DABG" or "MAS5"; of dimension length(unique(probeNames(object))) x ncol(object) if method="PSDABG") with p-values for P/A Calls.

Author(s)

Benilton Carvalho

References

Clark et al. Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol (2007) vol. 8 (4) pp. R64

Liu, W. M. and Mei, R. and Di, X. and Ryder, T. B. and Hubbell, E. and Dee, S. and Webster, T. A. and Harrington, C. A. and Ho, M. H. and Baid, J. and Smeekens, S. P. (2002) Analysis of high density expression microarrays with signed-rank call algorithms, Bioinformatics, 18(12), pp. 1593–1599.

Liu, W. and Mei, R. and Bartell, D. M. and Di, X. and Webster, T. A. and Ryder, T. (2001) Rank-based algorithms for analysis of microarrays, Proceedings of SPIE, Microarrays: Optical Technologies and Informatics, 4266.

Affymetrix (2002) Statistical Algorithms Description Document, Affymetrix Inc., Santa Clara, CA, whitepaper. http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf

Examples

## Not run: 
if (require(oligoData) & require(pd.huex.1.0.st.v2)){
  data(affyExonFS)
  ## Get only 2 samples for example
  dabgP = paCalls(affyExonFS[, 1:2])
  dabgPS = paCalls(affyExonFS[, 1:2], "PSDABG")
  head(dabgP) ## for probe
  head(dabgPS) ## for probeset
}

## End(Not run)

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: oligoClasses
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
Welcome to oligoClasses version 1.38.0
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

================================================================================
Welcome to oligo version 1.40.2
================================================================================
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
Loading required package: oligoData
Loading required package: pd.huex.1.0.st.v2
Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'oligoData'
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'pd.huex.1.0.st.v2'

oligo documentation built on Nov. 8, 2020, 6:52 p.m.